Whole genome sequencing of infected wheat using MinION

Fungal diseases of plants are responsible for major losses in agriculture, highlighting the need for rapid and accurate identification of plant pathogens. Disease outcomes are often defined not only by the main pathogen but are influenced by diverse microbial communities known as the microbiome at sites of infection. Here we present the first use of whole genome sequencing from a portable DNA sequencing device as a method for detection of fungal pathogens from wheat (Triticum aestivum). The data revealed that our method is robust and applicable to the diagnosis of fungal diseases including wheat stripe rust (caused by Puccinia striiformis f. sp. tritici), septoria tritici blotch (caused by Zymoseptoria tritici) and yellow leaf spot (caused by Pyrenophora tritici repentis). We also identified a bacterial genus Pseudomonas co-present with Puccinia and Zymoseptoria infections but not Pyrenophora infections. One limitation of the method is the over-representation of redundant wheat genome sequences in the sample. This could be addressed by amplicon-based sequencing approaches in future studies. Our work outlines a new approach for detection of a broad range of plant pathogens and associated microbes using a portable sequencer, providing the basis for future development of a system for on-site disease monitoring.